[gmx-users] combined ED analysis

[Anton Feenstra]

vincenzo venditti wrote:

> Dear list,
> I want to value the effect of 4 ligands (of various bilogical activities) on 
> the dynamic properties of a protein sistem. Then I've performed MD 
> simulations (4 ns) of each sistem and I've cheked the sampling for each 
> simulation computing the eigenvector overlaps and the cosine contenents.
> Then I've concatenated all trajectories together to construct the covariance 
> matrix and I've calculated the averaged projections and the rmsf of the 
> separate trajectories VS the eigenvector index.
> Now, in the light of the recent works of Dr. B. Hess [Phys. Rev. E 62, 8438 
> (2000); Phys. Rev. E 65, 031900 (2002)], can I to analyze the differences in 
> fluctuations along eigenvectors in which the separate trajectories show 
> different averaged projections?

In principle, you can. In practice, two runs of the *same* system will also 
show to some extent different averages and fluctuations. If you want to be 
(more) sure about real differences caused by your ligand binding, you could 
(or should) run several runs for each ligand (using different random 
starting velocities), preferably of at least 1ns, and 4ns would be great, 
and look at average differences between the groups of runs for the ligands.

I've used this, for example, to trace dynamic effects of mutations to the 
region around the active site, and shown that the rest of the protein 
remains unaffected. I used between 5-10 runs of 1-5 ns each for each 
mutant. (And, using 20-30 runs per ligand I did the same for three ligands, 
to show protein dynamics in that case was *not* influenced by ligand binding.)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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